Tracking live brain activity with the new NeuBtracker open-source microscope

A team of scientists from the Helmholtz Zentrum München and the Technical University of Munich (TUM) has successfully developed a new type of microscope. The so-called NeuBtracker is an open source microscope that allows to observe neuronal activities of zebrafish without perturbing their behavior. This is opening up completely new perspectives for science, because now it will be possible to track natural behavior while simultaneously imaging neuronal activity in the brain.

NeuBtracker* is equipped with two cameras: One tracks the unrestrained behavior of the zebrafish larva while the other automatically remains pointed at the transparent head, and consequently the brain, to record fluorescence images. “This approach makes it possible to observe neuronal activity during unrestrained behavior. We can test the larvae in different environmental conditions and can immediately analyze the effects,” says Prof. Dr. Gil Westmeyer from the Institutes of Biological and Medical Imaging (IBMI) and Developmental Genetics (IDG) at the Helmholtz Zentrum München as well as the Department of Nuclear Medicine and Munich School of Bioengineering (MSB) at the Technical University of Munich (TUM).

For example, by adding substances that influence metabolism, it is possible to observe resulting neuronal events in the brain in vivo. “Now we can finally simultaneously observe the effects of physiologically active substances on the behavior and brain activity,” states Panagiotis Symvoulidis from the TUM and the Helmholtz Zentrum München and the study’s first author. “The selective expression of fluorescent sensor proteins allows us to detect the activity of particular neurons.” “Consequently we can see exactly which areas in the brain are active during specific behaviors,” adds Dr. Antonella Lauri from Westmeyer’s team.

A microscope that anyone can build

The new instrument is a so-called open-source microscope. This means that instructions on how to build the microscope are available to everyone on the web ( “We wanted to give our scientific colleagues the possibility to build their own NeuBtracker because we had been waiting for such a device for years,” Westmeyer explains. “It is finally possible to see the effects of pharmacological substances on the behavior and the neuronal activity – or other cellular signal processing events – at the same time and across an entire organism. This systemic approach enables us to make new discoveries and we will for example seek to use this device in drug discovery and metabolic research,” Westmeyer adds.

The Helmholtz “Imaging and Curing Environmental Metabolic Diseases” Alliance (ICEMED) and the ERC Starting Grant to Gil Westmeyer supported the interdisciplinary project, in which also the Institute of Neuroscience and the Chair for Computer Aided Medical Procedures & Augmented Reality, as well as the Munich School of Bioengineering (MSB) of TUM participated.

Further information

Original publication: Symvoulidis P. et al (2017) NeuBtracker – imaging neurobehavioral dynamics in freely behaving fish Nature Methods DOI: 10.1038/NMETH.4459, online

Please read the full manuscript here (provided by the Springer’s SharedIt Initiative).

*NeuBtracker stands for neurobehavioral tracking microscope.

Prospective MR Image Alignment Between Breath-Holds: Application to Renal BOLD MRI



To present an image registration method for renal blood oxygen level-dependent (BOLD) measurements that enables semiautomatic assessment of parenchymal and medullary R2* changes under a functional challenge.


In a series of breath-hold acquisitions, three-dimensional data were acquired initially for prospective image registration of subsequent BOLD measurements. An algorithm for kidney alignment for BOLD renal imaging (KALIBRI) was implemented to detect the positions of the left and right kidney so that the kidneys were acquired in the subsequent BOLD measurement at consistent anatomical locations. Residual in-plane distortions were corrected retrospectively so that semiautomatic dynamic R2* measurements of the renal cortex and medulla become feasible. KALIBRI was tested in six healthy volunteers during a series of BOLD experiments, which included a 600- to 1000-mL water challenge.


Prospective image registration and BOLD imaging of each kidney was achieved within a total measurement time of about 17 s, enabling its execution within a single breath-hold. KALIBRI improved the registration by up to 35% as found with mutual information measures. In four volunteers, a medullary R2* decrease of up to 40% was observed after water ingestion.


KALIBRI improves the quality of two-dimensional time-resolved renal BOLD MRI by aligning local renal anatomy, which allows for consistent R2* measurements over many breath-holds.

Inge M. Kalis, David Pilutti, Axel J. Krafft, Jüurgen Hennig, and Michael Bock


Concise Review: Reprogramming, Behind the Scenes: Noncanonical Neural Stem Cell Signaling Pathways Reveal New, Unseen Regulators of Tissue Plasticity With Therapeutic Implications

Concise Review: Reprogramming, Behind the Scenes: Noncanonical Neural Stem Cell Signaling Pathways Reveal New, Unseen Regulators of Tissue Plasticity With Therapeutic Implications

Interest is great in the new molecular concepts that explain, at the level of signal transduction, the process of reprogramming. Usually, transcription factors with developmental importance are used, but these approaches give limited information on the signaling networks involved, which could reveal new therapeutic opportunities. Recent findings involving reprogramming by genetic means and sol- uble factors with well-studied downstream signaling mechanisms, including signal transducer and ac- tivator of transcription 3 (STAT3) and hairy and enhancer of split 3 (Hes3), shed new light into the molecular mechanisms that might be involved. We examine the appropriateness of common culture systems and their ability to reveal unusual (noncanonical) signal transduction pathways that actually operate in vivo. We then discuss such novel pathways and their importance in various plastic cell types, culminating in their emerging roles in reprogramming mechanisms. We also discuss a number of reprogramming paradigms (mouse induced pluripotent stem cells, direct conversion to neural stem cells, and in vivo conversion of acinar cells to b-like cells). Specifically for acinar-to-b-cell repro- gramming paradigms, we discuss the common view of the underlying mechanism (involving the Janus kinase-STAT pathway that leads to STAT3-tyrosine phosphorylation) and present alternative interpre- tations that implicate STAT3-serine phosphorylation alone or serine and tyrosine phosphorylation oc- curring in sequential order. The implications for drug design and therapy are important given that different phosphorylation sites on STAT3 intercept different signaling pathways. We introduce a new molecular perspective in the field of reprogramming with broad implications in basic, biotech- nological, and translational research.





Stem Cells Transl Med. 2015 Nov;4(11):1251-7. doi: 10.5966/sctm.2015-0105. Epub 2015 Sep 14.


PubMed link

Stonin1 mediates endocytosis of the proteoglycan NG2 and regulates focal adhesion dynamics and cell motility

Stonin1 mediates endocytosis of the proteoglycan NG2 and regulates focal adhesion dynamics and cell motility


Cellular functions, ranging from focal adhesion (FA) dynamics and cell motility to tumour growth, are orchestrated by signals cells receive from outside via cell surface receptors. Signalling is fine-tuned by the exo-endocytic cycling of these receptors to control cellular responses such as FA dynamics, which determine cell motility. How precisely endocytosis regulates turnover of the various cell surface receptors remains unclear. Here we identify Stonin1, an endocytic adaptor of unknown function, as a regulator of FA dynamics and cell motility, and demonstrate that it facilitates the internalization of the oncogenic proteoglycan NG2, a co-receptor of integrins and platelet-derived growth factor receptor. Embryonic fibroblasts obtained from Stonin1-deficient mice display a marked surface accumulation of NG2, increased cellular signalling and defective FA disassembly as well as altered cellular motility. These data establish Stonin1 as a specific adaptor for the endocytosis of NG2 and as an important factor for FA dynamics and cell migration.

Lysosomal sorting of amyloid-β by the SORLA receptor is impaired by a familial Alzheimer’s disease mutation

Lysosomal sorting of amyloid-β by the SORLA receptor is impaired by a familial Alzheimer’s disease mutation

Summary: SORLA/SORL1 is a unique neuronal sorting receptor for the amyloid precursor protein that has been causally implicated in both sporadic and autosomal dominant familial forms of Alzheimer’s disease (AD). Brain concentrations of SORLA are inversely correlated with amyloid-β (Aβ) in mouse models and AD patients, suggesting that increasing expression of this receptor could be a therapeutic option for decreasing the amount of amyloidogenic products in affected individuals. We characterize a new mouse model in which SORLA is overexpressed, and show a decrease in Aβ concentrations in mouse brain. We trace the underlying molecular mechanism to the ability of this receptor to direct lysosomal targeting of nascent Aβ peptides. Aβ binds to the amino-terminal VPS10P domain of SORLA, and this binding is impaired by a familial AD mutation in SORL1. Thus, loss of SORLA’s Aβ sorting function is a potential cause of AD in patients, and SORLA may be a new therapeutic target for AD drug development.

Caglayan S, Takagi-Niidome S, Liao F, Carlo AS, Schmidt V, Burgert T, Kitago Y, Füchtbauer EM, Füchtbauer A, Holtzman DM, Takagi J, Willnow TE.

Sci Transl Med. 2014 Feb 12;6(223):223ra20. doi: 10.1126/scitranslmed.3007747.

Hypothalamic UDP Increases in Obesity and Promotes Feeding via P2Y6-Dependent Activation of AgRP Neurons

Hypothalamic UDP Increases in Obesity and Promotes Feeding via P2Y6-Dependent Activation of AgRP Neurons

Activation of orexigenic AgRP-expressing neurons in the arcuate nucleus of the hypothalamus potently promotes feeding, thus defining new regulators of AgRP neuron activity could uncover potential novel targets for obesity treatment. Here, we demonstrate that AgRP neurons express the purinergic receptor 6 (P2Y6), which is activated by uridine-diphosphate (UDP). In vivo, UDP induces ERK phosphorylation and cFos expression in AgRP neurons and promotes action potential firing of these neurons in brain slice recordings. Consequently, central application of UDP promotes feeding, and this response is abrogated upon pharmacologic or genetic inhibition of P2Y6 as well as upon pharmacogenetic inhibition of AgRP neuron activity. In obese animals, hypothalamic UDP content is elevated as a consequence of increased circulating uridine concentrations. Collectively, these experiments reveal a potential regulatory pathway in obesity, where peripheral uridine increases hypothalamic UDP concentrations, which in turn can promote feeding via PY6-dependent activation of AgRP neurons.

Sophie M. Steculorum, Lars Paeger, Stephan Bremser, …, Marco Idzko, Peter Kloppenburg, Jens C. Brüning


Cell (2015) 162(6): 1404–1417.

PubMed Link:

Calcium neuroimaging in behaving zebrafish larvae using a turn-key light field camera

Calcium neuroimaging in behaving zebrafish larvae using a turn-key light field camera

Abstract. Reconstructing a three-dimensional scene from multiple simultaneously acquired perspectives (the light field) is an elegant scanless imaging concept that can exceed the temporal resolution of currently available scanning-based imaging methods for capturing fast cellular processes. We tested the performance of commercially available light field cameras on a fluorescent microscopy setup for monitoring calcium activity in the brain of awake and behaving reporter zebrafish larvae. The plenoptic imaging system could volumetrically resolve diverse neuronal response profiles throughout the zebrafish brain upon stimulation with an aversive odorant. Behavioral responses of the reporter fish could be captured simultaneously together with depth-resolved neuronal activity. Overall, our assessment showed that with some optimizations for fluorescence microscopy applications, commercial light field cameras have the potential of becoming an attractive alternative to custom-built systems to accelerate molecular imaging research on cellular dynamics.

Carlos Cruz Perez, Antonella Lauri, Panagiotis Symvoulidism Michele Cappetta, Arne Erdmann, Gil Gregor Westmeyer

Journal of Biomedical Optics (2015) 20(9): 096009.

PubMed link:

Triple-Quantum-Filtered Sodium Imaging at 9.4 Tesla

Mitochondrial Dynamics Controlled by Mitofusins Regulate Agrp Neuronal Activity and Diet-Induced Obesity



Efficient acquisition of triple-quantum-filtered (TQF) sodium images at ultra-high field (UHF) strength.


A three-pulse preparation and a stack of double-spirals were used for the acquisition of TQF images at 9.4 Tesla. The flip angles of the TQ preparation were smoothly reduced toward the edge of k-space along the partition-encoding direction. In doing so, the specific absorption rate could be reduced while preserving the maximal signal intensity for the partitions most relevant for image contrast in the center of k-space. Simulations, phantom and in vivo measurements were used to demonstrate the usefulness of the proposed method.


A higher sensitivity (∼20%) was achieved compared to the standard acquisition without flip angle apodization. Signals from free sodium ions were successfully suppressed irrespective of the amount of apodization used. B0 corrected TQF images with a nominal resolution of 5 × 5 × 5 mm3 and an acceptable signal-to-noise ratio could be acquired in vivo within 21 min.


Conventional TQF in combination with flip angle apodization permits to exploit more efficiently the increased sensitivity available at 9.4T. Magn Reson Med, 2015. © 2015 Wiley Periodicals, Inc.

Mirkes C, Shajan G, Bause J, Buckenmaier K, Hoffmann J, Scheffler K.


Orientation dependence of magnetization transfer parameters in human white matter

Quantification of magnetization-transfer (MT) experiments is typically based on a model comprising a liquid pool “a” of free water and a semisolid pool “b” of motionally restricted macromolecules or membrane compounds. By a comprehensive fitting approach, high qualityMT parameter maps of the human brain are obtained. In particular, a distinct correlation between the diffusion-tensor orientation with respect to the B0-magnetic field and the apparent transverse relaxation time, T2 b , of the semisolid pool (i.e., thewidth of its absorption line) is observed. This orientation dependence is quantitatively explained by a refined dipolar lineshape for pool b that explicitly considers the specific geometrical arrangement of lipid bilayers wrapped around a cylindrical axon. The model inherently reduces themyelinmembrane to its lipid constituents, which ismotivated by previous studies on efficient interaction sites (e.g., cholesterol or galactocerebrosides) in themyelinmembrane and on the origin of ultrashort T2 signals in cerebral white matter. The agreement betweenMT orientation effects and corresponding forward simulations using empirical diffusion imaging results as input as well as results from fits employing the novel lineshape support previous suggestions that the fiber orientation distribution in a voxel can bemodeled
as a scaled Bingham distribution.

André Pampel, Dirk K. Müller, Alfred Anwander, Henrik Marschner, Harald E. Möller


NeuroImage (2015) 114: 136-146.

PubMed Link:öller+orientation+dependance

High-Resolution Quantitative Sodium Imaging at 9.4 Tesla

Investigation of the feasibility to perform highresolution quantitative sodium imaging at 9.4 Tesla (T).
A proton patch antenna was combined with a sodium birdcage coil to provide a proton signal without compromising the efficiency of the X-nucleus coil. Sodium density weighted images with a nominal resolution of 1  1  5 mm3 were acquired within 30 min with an ultrashort echo time sequence. The methods used for signal calibration as well as for B0, B1, and off-resonance correction were verified on a phantom and five healthy volunteers.
An actual voxel volume of roughly 40 mL could be achieved at 9.4T, while maintaining an acceptable signal-tonoise ratio (8 for brain tissue and 35 for cerebrospinal fluid). The measured mean sodium concentrations for gray and white matter were 3662 and 3161 mmol/L of wet tissue, which
are comparable to values previously reported in the literature.
The reduction of partial volume effects is essential for accurate measurement of the sodium concentration in the human brain. Ultrahigh field imaging is a viable tool to achieve this goal due to its increased sensitivity.

Christian C. Mirkes, Jens Hoffmann, G. Shajan, Rolf Pohmann,
and Klaus Scheffler

Magn Reson Med. (2015) Apr 4

PubMed Link: